******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/135/135.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11498 1.0000 500 11750 1.0000 500 12076 1.0000 500 20665 1.0000 500 20753 1.0000 500 21223 1.0000 500 21469 1.0000 500 21715 1.0000 500 22437 1.0000 500 23010 1.0000 500 23137 1.0000 500 2317 1.0000 500 23586 1.0000 500 24174 1.0000 500 24828 1.0000 500 25052 1.0000 500 25254 1.0000 500 267964 1.0000 500 269423 1.0000 500 2923 1.0000 500 3206 1.0000 500 3694 1.0000 500 3811 1.0000 500 3842 1.0000 500 41521 1.0000 500 4445 1.0000 500 5233 1.0000 500 6233 1.0000 500 7029 1.0000 500 7193 1.0000 500 8500 1.0000 500 8535 1.0000 500 8775 1.0000 500 9265 1.0000 500 953 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/135/135.seqs.fa -oc motifs/135 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 35 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.222 G 0.255 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.222 G 0.255 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 31 llr = 321 E-value = 2.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 143163161:3312:551371 pos.-specific C 5225345:283353a428719 probability G 113:::4:2:21:3:1::::: matrix T 33241413622342::4::2: bits 2.2 * 2.0 * 1.7 * 1.5 * * * Relative 1.3 * * ** * Entropy 1.1 * * ** * (14.9 bits) 0.9 * * ** **** 0.7 * ** * * * ** **** 0.4 * ******* * ******* 0.2 ** ******* ** ******* 0.0 --------------------- Multilevel CAGCATCATCAACCCAACCAC consensus TTATCCGT CCTG CT A sequence C A T A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 23137 71 3.78e-09 GCGTCACCAA TAGCACCATCTACTCCACCAC CACCCAAACA 267964 455 4.72e-08 GAACATCCTC TCATCCCATCCCTCCCACCAC CTATCCGCGA 41521 458 5.65e-08 GGGCGGGAAC TTCCAACATCAACTCAACAAC GTCTGCACAA 11498 436 3.26e-07 ATCTCTCACC CTCCACGTCCTACTCATCCAC AGCCGACACC 3694 378 4.96e-07 ATATTACCAA TATCATCATCAATCCACCCTC CTTAGCCAGG 8500 110 6.49e-07 ATCGGAGAGG TTGTTTGAGCCACCCCACCAC CTCCGCGTGC 25052 68 1.55e-06 TTCGGTCTGC CTCCTTCTTCGCCCCCCCAAC CAACGCTTCC 2317 452 2.46e-06 AGAGAAGTAC GAATACCATTTTCCCCTCCAC ACTCTTCGCT 7193 24 2.75e-06 TCACCCAAGG TAGTATTATCATCGCCTCCTC CCTCATATCC 8535 446 3.41e-06 AGCTAAAAGA CATCATGTTCATATCAAACAC AATAGGTCGT 6233 106 3.41e-06 CGGTTGTCGT CGCCATCATCGTCGCCACACC GACGAACACC 21715 474 3.41e-06 CTACTTTTCT CCTCCTCTGCAACACAACCCC CTGCCC 7029 23 4.21e-06 CAATCATGGA GAGTACCTTCAACACATCCAA ACCTGACCCA 2923 15 6.93e-06 AGGAAGATTC CTCTCCGTTTCGTGCAACCAC CCCAGCAGAG 21223 479 6.93e-06 TTGGACGGGC CTTTCCTATCCTCTCAACCAA C 21469 403 7.63e-06 CGTTCTATCG CTACACAAGCTTCCCATCATC ACCGTTGGTC 953 331 8.38e-06 CGTCGCTCCT CAACCTCAACGTTGCCTCCAA ACGACGAACG 9265 136 8.38e-06 GGATCTCGGG CTGTCTCTTCGGTGCACCAAC ACCAGTTCCT 5233 456 8.38e-06 ATTTATTGGA CATTTTCTTTCTTACAACAAC CCCTTACTCG 11750 455 9.20e-06 ACATATTATG ACATAAGATCCCCACATACAC CGTCGCTGCA 23010 6 1.10e-05 GGCGG CACCATCACCATTGCCTGAAC CGACGTCATC 269423 364 1.21e-05 GTTGGCACCA TGGCAAGAGCACTCCGACCAC ACGCTTCTGC 24828 346 1.32e-05 TTTTCACAGT CAACAACACTCCATCCTCCTC TCTTTGCTAG 3842 450 1.44e-05 ACGACGGCCA CAGCACGAACTCTACGCCAAC TGCCAACCCC 8775 142 2.36e-05 GTGATCAAAG CAATTAGATTGCCCCCAAAAC GCCGAAGAAG 25254 365 2.36e-05 ATGCAGGCCA TCAACAAACCCACTCACCCAC CTGAGCGACC 20665 374 2.36e-05 TCCGAGCGCG ATGAACGATCCCTGCCTCATC AAACGCTCCA 23586 43 2.55e-05 TTTGTCTCGT TTGTAAACCCTCCACCACCAC CGTTGATGGC 12076 428 3.72e-05 GAGTTCATAT CCGTCCATACGATGCAACCCC AACTTTGACA 3811 383 4.29e-05 GAGCGCGAAA TATAAAGAGCACACCATCCAA CAACGGCTAC 3206 348 7.82e-05 GCGATTTTGT CCCACTGTTTAAAACAAACAC CATTTTTTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23137 3.8e-09 70_[+1]_409 267964 4.7e-08 454_[+1]_25 41521 5.6e-08 457_[+1]_22 11498 3.3e-07 435_[+1]_44 3694 5e-07 377_[+1]_102 8500 6.5e-07 109_[+1]_370 25052 1.6e-06 67_[+1]_412 2317 2.5e-06 451_[+1]_28 7193 2.7e-06 23_[+1]_456 8535 3.4e-06 445_[+1]_34 6233 3.4e-06 105_[+1]_374 21715 3.4e-06 473_[+1]_6 7029 4.2e-06 22_[+1]_457 2923 6.9e-06 14_[+1]_465 21223 6.9e-06 478_[+1]_1 21469 7.6e-06 402_[+1]_77 953 8.4e-06 330_[+1]_149 9265 8.4e-06 135_[+1]_344 5233 8.4e-06 455_[+1]_24 11750 9.2e-06 454_[+1]_25 23010 1.1e-05 5_[+1]_474 269423 1.2e-05 363_[+1]_116 24828 1.3e-05 345_[+1]_134 3842 1.4e-05 449_[+1]_30 8775 2.4e-05 141_[+1]_338 25254 2.4e-05 364_[+1]_115 20665 2.4e-05 373_[+1]_106 23586 2.6e-05 42_[+1]_437 12076 3.7e-05 427_[+1]_52 3811 4.3e-05 382_[+1]_97 3206 7.8e-05 347_[+1]_132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=31 23137 ( 71) TAGCACCATCTACTCCACCAC 1 267964 ( 455) TCATCCCATCCCTCCCACCAC 1 41521 ( 458) TTCCAACATCAACTCAACAAC 1 11498 ( 436) CTCCACGTCCTACTCATCCAC 1 3694 ( 378) TATCATCATCAATCCACCCTC 1 8500 ( 110) TTGTTTGAGCCACCCCACCAC 1 25052 ( 68) CTCCTTCTTCGCCCCCCCAAC 1 2317 ( 452) GAATACCATTTTCCCCTCCAC 1 7193 ( 24) TAGTATTATCATCGCCTCCTC 1 8535 ( 446) CATCATGTTCATATCAAACAC 1 6233 ( 106) CGCCATCATCGTCGCCACACC 1 21715 ( 474) CCTCCTCTGCAACACAACCCC 1 7029 ( 23) GAGTACCTTCAACACATCCAA 1 2923 ( 15) CTCTCCGTTTCGTGCAACCAC 1 21223 ( 479) CTTTCCTATCCTCTCAACCAA 1 21469 ( 403) CTACACAAGCTTCCCATCATC 1 953 ( 331) CAACCTCAACGTTGCCTCCAA 1 9265 ( 136) CTGTCTCTTCGGTGCACCAAC 1 5233 ( 456) CATTTTCTTTCTTACAACAAC 1 11750 ( 455) ACATAAGATCCCCACATACAC 1 23010 ( 6) CACCATCACCATTGCCTGAAC 1 269423 ( 364) TGGCAAGAGCACTCCGACCAC 1 24828 ( 346) CAACAACACTCCATCCTCCTC 1 3842 ( 450) CAGCACGAACTCTACGCCAAC 1 8775 ( 142) CAATTAGATTGCCCCCAAAAC 1 25254 ( 365) TCAACAAACCCACTCACCCAC 1 20665 ( 374) ATGAACGATCCCTGCCTCATC 1 23586 ( 43) TTGTAAACCCTCCACCACCAC 1 12076 ( 428) CCGTCCATACGATGCAACCCC 1 3811 ( 383) TATAAAGAGCACACCATCCAA 1 3206 ( 348) CCCACTGTTTAAAACAAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16800 bayes= 9.78661 E= 2.8e-009 -199 130 -198 28 71 -20 -198 28 1 2 34 -46 -99 102 -1160 65 118 39 -1160 -105 1 68 -1160 54 -99 102 48 -205 133 -278 -1160 28 -141 -46 -66 112 -1160 186 -1160 -46 33 39 -40 -46 33 54 -198 12 -99 122 -1160 41 -18 39 2 -24 -1160 217 -1160 -1160 101 92 -198 -1160 92 -46 -1160 41 -99 192 -298 -1160 33 161 -1160 -1160 153 -120 -1160 -72 -99 197 -1160 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 2.8e-009 0.064516 0.548387 0.064516 0.322581 0.419355 0.193548 0.064516 0.322581 0.258065 0.225806 0.322581 0.193548 0.129032 0.451613 0.000000 0.419355 0.580645 0.290323 0.000000 0.129032 0.258065 0.354839 0.000000 0.387097 0.129032 0.451613 0.354839 0.064516 0.645161 0.032258 0.000000 0.322581 0.096774 0.161290 0.161290 0.580645 0.000000 0.806452 0.000000 0.193548 0.322581 0.290323 0.193548 0.193548 0.322581 0.322581 0.064516 0.290323 0.129032 0.516129 0.000000 0.354839 0.225806 0.290323 0.258065 0.225806 0.000000 1.000000 0.000000 0.000000 0.516129 0.419355 0.064516 0.000000 0.483871 0.161290 0.000000 0.354839 0.129032 0.838710 0.032258 0.000000 0.322581 0.677419 0.000000 0.000000 0.741935 0.096774 0.000000 0.161290 0.129032 0.870968 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][AT][GAC][CT][AC][TCA][CG][AT]TC[AC][ACT][CT][CGAT]C[AC][AT]C[CA]AC -------------------------------------------------------------------------------- Time 13.00 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 16 llr = 193 E-value = 7.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4::5:33:::::31: pos.-specific C ::6::a::4:34:1:1 probability G a5295:74:a51a568 matrix T :121::136:34:131 bits 2.2 * 2.0 * * * * 1.7 * * * * * 1.5 * * * * * Relative 1.3 * * * * * Entropy 1.1 * * * ** * * (17.4 bits) 0.9 * **** ** * * 0.7 ******* ** ** ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel GGCGACGGTGGCGGGG consensus A G ATC CT AT sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23137 246 2.26e-09 AGAGGGCACC GGCGGCGGCGGCGGGG CTTCTTGTGG 23586 77 4.24e-09 TGATGGCATT GGCGGCGGCGGTGGGG CTGTTGCTGC 25254 282 1.38e-07 ATGATGTGTT GGCGACGTTGTCGGTG TCGGTCGGCA 24174 342 4.60e-07 AGAGCCAGAT GACGACGATGCCGTGG ATGGATGGAG 8535 74 5.09e-07 GTAAACTGTA GACGACAGTGGCGATG CTCAAGGGAA 269423 38 7.98e-07 CGTTTGTTGC GGCGACGTTGCTGCTG CAGTTTGGAG 21223 34 7.98e-07 TCATCTGAAA GTCGACATTGCCGGGG GTGATGACAA 3842 342 8.80e-07 GTATCGTCGC GGCGGCGGTGCGGTGG CGTGTGATGT 20753 151 1.20e-06 CATGATTTGT GGTGACGATGGTGGAG ATCAGCTTGG 8500 339 3.07e-06 GACGTTTGGG GAGGACGACGGGGAGG ACGGCTACTT 11498 174 3.07e-06 AGAATGCGCG GAGGGCAGTGGTGGGT GATGGGCAGA 3206 68 4.71e-06 GGATGATGAG GGTTGCGGCGGCGAGG ATTGCAATTG 22437 290 4.71e-06 GTGAGAGGTG GACGGCGTCGTCGGTC GTCGTTTCGA 23010 69 5.06e-06 GCACTCAAGA GACGACGACGTTGCGT CAGCAACTCA 7029 371 6.12e-06 AGAGGATGTT GTTGGCAGTGGTGGAG CATACATCAG 2317 353 6.90e-06 GGAGACGGGA GGGGGCTTTGTTGAGG GGTCAACGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23137 2.3e-09 245_[+2]_239 23586 4.2e-09 76_[+2]_408 25254 1.4e-07 281_[+2]_203 24174 4.6e-07 341_[+2]_143 8535 5.1e-07 73_[+2]_411 269423 8e-07 37_[+2]_447 21223 8e-07 33_[+2]_451 3842 8.8e-07 341_[+2]_143 20753 1.2e-06 150_[+2]_334 8500 3.1e-06 338_[+2]_146 11498 3.1e-06 173_[+2]_311 3206 4.7e-06 67_[+2]_417 22437 4.7e-06 289_[+2]_195 23010 5.1e-06 68_[+2]_416 7029 6.1e-06 370_[+2]_114 2317 6.9e-06 352_[+2]_132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=16 23137 ( 246) GGCGGCGGCGGCGGGG 1 23586 ( 77) GGCGGCGGCGGTGGGG 1 25254 ( 282) GGCGACGTTGTCGGTG 1 24174 ( 342) GACGACGATGCCGTGG 1 8535 ( 74) GACGACAGTGGCGATG 1 269423 ( 38) GGCGACGTTGCTGCTG 1 21223 ( 34) GTCGACATTGCCGGGG 1 3842 ( 342) GGCGGCGGTGCGGTGG 1 20753 ( 151) GGTGACGATGGTGGAG 1 8500 ( 339) GAGGACGACGGGGAGG 1 11498 ( 174) GAGGGCAGTGGTGGGT 1 3206 ( 68) GGTTGCGGCGGCGAGG 1 22437 ( 290) GACGGCGTCGTCGGTC 1 23010 ( 69) GACGACGACGTTGCGT 1 7029 ( 371) GTTGGCAGTGGTGGAG 1 2317 ( 353) GGGGGCTTTGTTGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 11.3725 E= 7.7e-003 -1064 -1064 197 -1064 55 -1064 97 -109 -1064 149 -44 -51 -1064 -1064 188 -209 96 -1064 97 -1064 -1064 217 -1064 -1064 -4 -1064 143 -209 -4 -1064 78 23 -1064 76 -1064 123 -1064 -1064 197 -1064 -1064 17 97 -9 -1064 98 -103 71 -1064 -1064 197 -1064 -4 -83 97 -109 -104 -1064 129 -9 -1064 -183 167 -109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 7.7e-003 0.000000 0.000000 1.000000 0.000000 0.375000 0.000000 0.500000 0.125000 0.000000 0.625000 0.187500 0.187500 0.000000 0.000000 0.937500 0.062500 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.687500 0.062500 0.250000 0.000000 0.437500 0.312500 0.000000 0.375000 0.000000 0.625000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.437500 0.125000 0.437500 0.000000 0.000000 1.000000 0.000000 0.250000 0.125000 0.500000 0.125000 0.125000 0.000000 0.625000 0.250000 0.000000 0.062500 0.812500 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GA]CG[AG]C[GA][GTA][TC]G[GCT][CT]G[GA][GT]G -------------------------------------------------------------------------------- Time 25.75 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 26 llr = 237 E-value = 1.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 51::2::1::32 pos.-specific C :::::3::::2: probability G 361a7:a::633 matrix T 339:17:9a424 bits 2.2 2.0 * * * 1.7 * * * 1.5 ** *** Relative 1.3 ** *** Entropy 1.1 ** **** (13.1 bits) 0.9 ** ***** 0.7 ********* 0.4 ********** * 0.2 ********** * 0.0 ------------ Multilevel AGTGGTGTTGGT consensus GT C TAG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 20753 113 2.84e-07 TGGCCCGTTG AGTGGTGTTGAT TGATTACGAC 25254 135 6.56e-07 CGTACAAAGT AGTGGTGTTTGG TTGACGGCCG 24174 211 6.56e-07 TATTGCATAG AGTGGTGTTGCT ACGAACACAG 8535 151 6.05e-06 AAGGTTGAGC TGTGGTGTTGTT TGTAGGCACG 24828 277 7.14e-06 CAAATCTATA ATTGGTGTTTAT GAGCTAAACG 21715 11 1.24e-05 ACCTAAGCCT GTTGGTGTTGCT GAGAAGGCCA 21469 54 1.24e-05 CTCCTTGTTC GTTGGTGTTTGG ACACTTTCGT 5233 118 1.58e-05 TAGGATTCCC AGTGATGTTGTG GAGGTATCGG 21223 250 1.75e-05 ACGGAGATCG TGTGGCGTTGGA GGCGGTTGTT 7193 317 1.95e-05 GTTTGTCGGA TGTGATGTTGAT GGTTGATGTG 3206 121 1.95e-05 CGATGCACCG AGTGACGTTGGG TAGCGTCCTG 953 8 2.16e-05 GTATCAA GTTGGTGTTTGA CGTAACAAAT 4445 178 2.37e-05 ATCGTATTGT ATTGGTGTTTTA AGGTGCCGAG 3842 365 2.37e-05 TGGCGTGTGA TGTGGCGTTGAA GTGGCAGGGG 8500 281 2.61e-05 GCTTGTGGCT TGTGGCGTTTCG CTGTGGTTGC 25052 424 2.61e-05 CAATGACTTC AGTGACGTTTGT TTGGTATCCG 2317 258 2.87e-05 GTTGGCGACT AATGGTGTTTGT TCTGATGGAG 7029 425 3.73e-05 TTGGCTGACC ATTGTTGTTGAT CAACTTAGCT 8775 468 4.03e-05 CGAACAACCA GGTGTTGTTGGA AGCACAACCA 11498 343 4.77e-05 CTCCTCCTGT AGTGTCGTTTGG GGCTGTGCTG 41521 20 6.51e-05 ACGGCACAAA GATGGTGTTGTG ATGTGCACAA 23137 338 7.50e-05 GAGGTGTGCT TGGGGTGTTGCT GTTGTCGTCC 23586 401 1.16e-04 CAATTCGCAC GGTGGCGATGAG GTAGACAGCG 11750 19 1.43e-04 GAATGATGCA TGTGATGATGAT AATGTTGTGT 269423 169 1.57e-04 AGCTATTTGA ATGGGTGTTTTA CTCTCTGTAG 3811 100 1.65e-04 TTGTTCCGCT GTTGCTGTTTCG TGCCCCATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20753 2.8e-07 112_[+3]_376 25254 6.6e-07 134_[+3]_354 24174 6.6e-07 210_[+3]_278 8535 6e-06 150_[+3]_338 24828 7.1e-06 276_[+3]_212 21715 1.2e-05 10_[+3]_478 21469 1.2e-05 53_[+3]_435 5233 1.6e-05 117_[+3]_371 21223 1.7e-05 249_[+3]_239 7193 1.9e-05 316_[+3]_172 3206 1.9e-05 120_[+3]_368 953 2.2e-05 7_[+3]_481 4445 2.4e-05 177_[+3]_311 3842 2.4e-05 364_[+3]_124 8500 2.6e-05 280_[+3]_208 25052 2.6e-05 423_[+3]_65 2317 2.9e-05 257_[+3]_231 7029 3.7e-05 424_[+3]_64 8775 4e-05 467_[+3]_21 11498 4.8e-05 342_[+3]_146 41521 6.5e-05 19_[+3]_469 23137 7.5e-05 337_[+3]_151 23586 0.00012 400_[+3]_88 11750 0.00014 18_[+3]_470 269423 0.00016 168_[+3]_320 3811 0.00016 99_[+3]_389 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=26 20753 ( 113) AGTGGTGTTGAT 1 25254 ( 135) AGTGGTGTTTGG 1 24174 ( 211) AGTGGTGTTGCT 1 8535 ( 151) TGTGGTGTTGTT 1 24828 ( 277) ATTGGTGTTTAT 1 21715 ( 11) GTTGGTGTTGCT 1 21469 ( 54) GTTGGTGTTTGG 1 5233 ( 118) AGTGATGTTGTG 1 21223 ( 250) TGTGGCGTTGGA 1 7193 ( 317) TGTGATGTTGAT 1 3206 ( 121) AGTGACGTTGGG 1 953 ( 8) GTTGGTGTTTGA 1 4445 ( 178) ATTGGTGTTTTA 1 3842 ( 365) TGTGGCGTTGAA 1 8500 ( 281) TGTGGCGTTTCG 1 25052 ( 424) AGTGACGTTTGT 1 2317 ( 258) AATGGTGTTTGT 1 7029 ( 425) ATTGTTGTTGAT 1 8775 ( 468) GGTGTTGTTGGA 1 11498 ( 343) AGTGTCGTTTGG 1 41521 ( 20) GATGGTGTTGTG 1 23137 ( 338) TGGGGTGTTGCT 1 23586 ( 401) GGTGGCGATGAG 1 11750 ( 19) TGTGATGATGAT 1 269423 ( 169) ATGGGTGTTTTA 1 3811 ( 100) GTTGCTGTTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17115 bayes= 9.89153 E= 1.7e-001 85 -1134 8 1 -174 -1134 127 21 -1134 -1134 -173 179 -1134 -1134 197 -1134 -42 -253 136 -121 -1134 28 -1134 145 -1134 -1134 197 -1134 -174 -1134 -1134 179 -1134 -1134 -1134 191 -1134 -1134 118 67 7 -21 44 -47 -15 -1134 44 67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 26 E= 1.7e-001 0.461538 0.000000 0.269231 0.269231 0.076923 0.000000 0.615385 0.307692 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 1.000000 0.000000 0.192308 0.038462 0.653846 0.115385 0.000000 0.269231 0.000000 0.730769 0.000000 0.000000 1.000000 0.000000 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.576923 0.423077 0.269231 0.192308 0.346154 0.192308 0.230769 0.000000 0.346154 0.423077 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AGT][GT]TGG[TC]GTT[GT][GA][TGA] -------------------------------------------------------------------------------- Time 37.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11498 1.08e-06 173_[+2(3.07e-06)]_153_\ [+3(4.77e-05)]_16_[+3(8.61e-05)]_53_[+1(3.26e-07)]_44 11750 3.36e-03 454_[+1(9.20e-06)]_25 12076 2.02e-01 427_[+1(3.72e-05)]_52 20665 4.53e-02 373_[+1(2.36e-05)]_106 20753 7.31e-06 112_[+3(2.84e-07)]_1_[+2(4.78e-05)]_\ 9_[+2(1.20e-06)]_334 21223 2.05e-06 33_[+2(7.98e-07)]_200_\ [+3(1.75e-05)]_217_[+1(6.93e-06)]_1 21469 1.28e-03 12_[+3(5.59e-05)]_29_[+3(1.24e-05)]_\ 337_[+1(7.63e-06)]_77 21715 2.06e-04 10_[+3(1.24e-05)]_17_[+3(5.59e-05)]_\ 422_[+1(3.41e-06)]_6 22437 8.11e-03 289_[+2(4.71e-06)]_195 23010 8.29e-04 5_[+1(1.10e-05)]_42_[+2(5.06e-06)]_\ 416 23137 3.50e-11 70_[+1(3.78e-09)]_154_\ [+2(2.26e-09)]_76_[+3(7.50e-05)]_151 2317 8.65e-06 257_[+3(2.87e-05)]_83_\ [+2(6.90e-06)]_83_[+1(2.46e-06)]_28 23586 3.18e-07 42_[+1(2.55e-05)]_13_[+2(4.24e-09)]_\ 408 24174 9.98e-06 58_[+2(2.53e-05)]_136_\ [+3(6.56e-07)]_119_[+2(4.60e-07)]_143 24828 1.28e-03 276_[+3(7.14e-06)]_57_\ [+1(1.32e-05)]_134 25052 3.53e-04 67_[+1(1.55e-06)]_335_\ [+3(2.61e-05)]_65 25254 6.48e-08 134_[+3(6.56e-07)]_135_\ [+2(1.38e-07)]_67_[+1(2.36e-05)]_115 267964 6.74e-04 454_[+1(4.72e-08)]_25 269423 2.29e-05 37_[+2(7.98e-07)]_310_\ [+1(1.21e-05)]_116 2923 1.11e-02 14_[+1(6.93e-06)]_465 3206 9.06e-05 67_[+2(4.71e-06)]_37_[+3(1.95e-05)]_\ 168_[+3(6.51e-05)]_35_[+1(7.82e-05)]_132 3694 2.47e-03 377_[+1(4.96e-07)]_102 3811 8.64e-03 382_[+1(4.29e-05)]_97 3842 5.62e-06 341_[+2(8.80e-07)]_7_[+3(2.37e-05)]_\ 73_[+1(1.44e-05)]_30 41521 8.55e-05 19_[+3(6.51e-05)]_426_\ [+1(5.65e-08)]_22 4445 4.20e-02 177_[+3(2.37e-05)]_311 5233 2.67e-04 117_[+3(1.58e-05)]_326_\ [+1(8.38e-06)]_24 6233 1.06e-02 105_[+1(3.41e-06)]_374 7029 1.57e-05 22_[+1(4.21e-06)]_327_\ [+2(6.12e-06)]_38_[+3(3.73e-05)]_64 7193 2.72e-04 23_[+1(2.75e-06)]_5_[+1(9.39e-05)]_\ 246_[+3(1.95e-05)]_172 8500 1.17e-06 109_[+1(6.49e-07)]_150_\ [+3(2.61e-05)]_46_[+2(3.07e-06)]_146 8535 2.77e-07 73_[+2(5.09e-07)]_61_[+3(6.05e-06)]_\ 283_[+1(3.41e-06)]_34 8775 9.59e-03 141_[+1(2.36e-05)]_305_\ [+3(4.03e-05)]_21 9265 2.89e-02 135_[+1(8.38e-06)]_344 953 2.29e-03 7_[+3(2.16e-05)]_311_[+1(8.38e-06)]_\ 149 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************